Alzheimer's is progressive and irreversible type of dementia, which causes degeneration and death of cells and their connections in the brain. AD worsens over time and greatly impacts patients' life and affects their important mental functions, including thinking, the ability to carry on a conversation, and judgment and response to environment. Clinically, there is no single test to effectively diagnose Alzheimer disease. However, computed tomography (CT) and magnetic resonance imaging (MRI) scans can be used to help in AD diagnosis by observing critical changes in the size of different brain areas, typically parietal and temporal lobes areas. In this work, an integrative mulitresolutional ensemble deep learning-based framework is proposed to achieve better predictive performance for the diagnosis of Alzheimer disease. Unlike ResNet, DenseNet and their variants proposed pipeline utilizes PartialNet in a hierarchical design tailored to AD detection using brain MRIs. The advantage of the proposed analysis system is that PartialNet diversified the depth and deep supervision. Additionally, it also incorporates the properties of identity mappings which makes it powerful in better learning due to feature reuse. Besides, the proposed ensemble PartialNet is better in vanishing gradient, diminishing forward-flow with low number of parameters and better training time in comparison to its counter network. The proposed analysis pipeline has been tested and evaluated on benchmark ADNI dataset collected from 379 subjects patients. Quantitative validation of the obtained results documented our framework's capability, outperforming state-of-the-art learning approaches for both multi-and binary-class AD detection.

We propose an automated, explainable artificial intelligence (xAI) system for age-related macular degeneration (AMD) diagnosis. Mimicking the physician's perceptions, the proposed xAI system is capable of deriving clinically meaningful features from optical coherence tomography (OCT) B-scan images to differentiate between a normal retina, different grades of AMD (early, intermediate, geographic atrophy (GA), inactive wet or active neovascular disease [exudative or wet AMD]), and non-AMD diseases. Particularly, we extract retinal OCT-based clinical imaging markers that are correlated with the progression of AMD, which include: (i) subretinal tissue, sub-retinal pigment epithelial tissue, intraretinal fluid, subretinal fluid, and choroidal hypertransmission detection using a DeepLabV3+ network; (ii) detection of merged retina layers using a novel convolutional neural network model; (iii) drusen detection based on 2D curvature analysis; (iv) estimation of retinal layers' thickness, and first-order and higher-order reflectivity features. Those clinical features are used to grade a retinal OCT in a hierarchical decision tree process. The first step looks for severe disruption of retinal layers' indicative of advanced AMD. These cases are analyzed further to diagnose GA, inactive wet AMD, active wet AMD, and non-AMD diseases. Less severe cases are analyzed using a different pipeline to identify OCT with AMD-specific pathology, which is graded as intermediate-stage or early-stage AMD. The remainder is classified as either being a normal retina or having other non-AMD pathology. The proposed system in the multi-way classification task, evaluated on 1285 OCT images, achieved 90.82% accuracy. These promising results demonstrated the capability to automatically distinguish between normal eyes and all AMD grades in addition to non-AMD diseases.

In recent years, the management and analysis of biological data have experienced exponential growth propelled by the relentless advancement of machine learning (ML) and artificial intelligence (AI) technologies. This is driven mainly by the remarkable ability and potentials of AI-based systems to craft sophisticated, yet effective, algorithms and analytical models tailored for the interpretation of biological information; thus, assist in making accurate predictions and/or decisions [1]. The surge in AI adoption is not unfounded; it's a response to the overwhelming increase in both the volume and acquisition rates of biological data.

Breast cancer is a prevalent and diverse type of cancer that exhibits unique clinicopathologic characteristics, making the correct identification of its subtype critical to providing targeted treatment and increasing survival rates. This identification process involves testing for the presence of four key molecular biomarkers, namely estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and antigen Ki67. For accurate diagnosis ,the expertise of a pathologist and immunohistochemistry is required. To overcome this diagnostic challenge, we present a novel approach based on a deep learning pipeline for automated classification. Our approach can detect tumor and non-tumoral regions of the HER2 biomarker. Our deep learning framework comprises a Dense Convolutional Network (DenseNet), which process whole slide images (WSIs) of breast tissues, dividing them into patches for input into the network. Moreover, our approach provides both patchwise and pixelwise classification and analyzes ten WSIs of breast cancer histology. Our proposed approach generates an image map that classifies slide images on the pixel-level, detecting the status of hormone HER2 receptor as either positive or negative. The obtained results show that our deep learning-based approach has the potential to enhance the pathologist’s capabilities in diagnosing histopathological images with automated classification.

Retinal disorders diagnosis is of immense importance for appropriate treatment, i.e., accurate personalized medicine. In this work, a multi-resolutional feature ensemble approach is developed for retinal image classification using optical coherence tomography (OCT) images. Particularly, feature-rich pipeline using pyramidal architecture is designed to extract features from multi-scale inputs using partially-connected networks (PCNet). In addition, higher-order reflectivity features are extracted from the input images and are fused with pyramidal features for classification. The advantage of the hierarchical PCNet structure is that it allowed our system to extract multi-scale information to help in such task, all-at-once classification of the normal and abnormal retina. Namely, the larger input sizes give more global information, while the small inputs focus on local details. Evaluation on public OCT data set of four classes (normal, diabetic macular edema (DME), choroidal neovascularization (CNV), and drusen) and comparison against recent networks demonstrates not only the advantages of the proposed architecture’s ability to produce feature-rich classification, but also highlights tangible advantages, such as network parameter reduction, enhanced feature learning and information flow, while reducing the risk of over fitting.

The thirteen papers in this special issue focus on open and interoperable artificial intelligence (AI) in computational pathology. Recent years have seen exponential advances in the quality of AI techniques in the medical filed. Particularly, AI/ML tools have been widely exploited pathological image analysis to examine and assess the function of human organs and/or to provide trustworthy prediction of diseases.

Prostate cancer (PC) is the most common cancer, a significant cause of morbidity, and is the second vital cancer that causes death in the US. Early PC detection is one of the major factors in decreasing mortality. We introduce a deep learning (DL) system for automated Gleason system grading (Gleason pattern (GP) and Gleason score (GS)) and grade groups (GG) using whole slide images (WSIs) of the digitized prostate biopsy specimens (PBSs). The DL is a pyramidal convolution neural network (CNN) approach consisting of progressively larger patch-sized shallow CNN to provide hierarchical information features. We used three patches sizes 100×100 (small), 150×150 (median), and 200×200 (large) pixels, so the pyramidal CNN affords us varying contextual features. The small patches give more local information, while the large patches provide global features. The patch-wise classification yields five probabilities representing the GP types from 1 to 5 at each pyramidal level. Then, we get the average for those three levels. We used three metrics to evaluate the GP classification diagnostic: recall, accuracy, and precision. The classification accuracy for the CNNL(large patches) is 0.77, the best among the three CNNs. The GG results are between 50% to 75% for recall. GG’s results are highlighted in our DL systems by comparing them with the current work.

Early detection and diagnosis of thyroid nodules are very important to rescue patients before the cancer spreads all over the patient’s body. A computer-aided diagnosis (CAD) system is proposed to detect the malignancy of thyroid nodules using magnetic resonance imaging (MRI) scans. This system extracts three descriptive features from T2-weighted (T2) MRI. These features are 1st-order reflectivity, 2nd-order reflectivity, and spherical harmonic. The 1st-order reflectivity is represented by sufficient statistics, (i.e. CDF percentiles), extracted from the cumulative distribution function (CDF) generated from it. After-ward, these features are fed to a neural network (NN) individually for diagnosis. Then, the classification outputs for these networks are fused using another NN for final diagnosis. The developed system is trained and tested using leave-one-subject-out (LOSO) cross-validation technique on MRI scans from 63 patients. The proposed fusion system shows incredible improvements in diagnostic accuracy, compared with other machine learning approach and a well-know pretrained deep learning network as well as individual feature classification. The overall sensitivity, specificity, F1-score, and accuracy of the proposed system are 91.3%, 95%, 91.3%, and 93.65%, respectively. The reported results, based on the fusion of reflectivity features as well as morphological feature, show the promise of the developed system in differentiating between benign and malignant thyroid nodules.

Alzheimer's disease (AD) is an irreversible and progressive disorder where a large number of brain cells and their connections degenerate and die, eventually destroy the memory and other important mental functions that affect memory, thinking, language, judgment, and behavior. Not a single test can effectively determine AD; however, CT and magnetic resonance imaging (MRI) can be used to observe the decrease in size of different areas (mainly temporal and parietal lobes). This paper proposes an integrative deep ensemble learning framework to obtain better predictive performance for AD diagnosis. Unlike DenseNet, we present a multiresolutional ensemble PartialNet tailored to Alzheimer detection using brain MRIs. PartialNet incorporates the properties of identity mappings, diversified depth as well as deep supervision, thus, considers feature reuse that in turn results in better learning. Additionally, the proposed ensemble PartialNet demonstrates better characteristics in terms of vanishing gradient, diminishing forward flow with better training time, and a low number of parameters compared with DenseNet. Experiments performed on benchmark AD neuroimaging initiative data set that showed considerable performance gain (2 + % ↑ $\uparrow $ ) and (1.2 + % ↑ $\uparrow $ ) for multiclass and binary class in AD detection in comparison to state-of-the-art methods.

A novel framework for the detection of radiation-induced lung injury (RILI) from 4D computed tomography (CT) has been proposed. Our framework performs 4D-CT lung fields segmentation, deformable image registration (DIR), extraction of textural and functional features, and classification of lung voxels using deep 3D convolutional neural networks (CNN). The 4D-CT images segmentation extracts the lung fields inside the exhale phase using our multi-scale Gaussian adaptive shape prior technique followed by label propagation to other 4D-CT phases using a newly developed adaptive shape model. Then, the 4D-CT DIR locally aligns consecutive phases of the respiratory cycle using the 3D Laplace equation for finding voxel correspondences between the iso-surfaces for the fixed and moving lungs and generalized Gaussian Markov random field (GGMRF) as an anatomical consistency constraint. In addition to common lung functionality features, such as ventilation and elasticity, specific regional textural features are estimated by modeling the segmented images as samples of a novel 7th-order contrast-offset-invariant Markov-Gibbs random field (MGRF). Finally, a deep 3D CNN is applied to distinguish between the injured and normal lung tissues. 4D-CT datasets collected from 13 patients, who undergone the radiation therapy (RT), have been used in the evaluation of the proposed framework. The experimental results show the promise of our framework.

To accurately segment pathological and healthy lungs for reliable computer-aided disease diagnostics, a stack of chest CT scans is modeled as a sample of a spatially inhomogeneous joint 3D Markov-Gibbs random field (MGRF) of voxel-wise lung and chest CT image signals (intensities). The proposed learnable MGRF integrates two visual appearance sub-models with an adaptive lung shape submodel. The first-order appearance submodel accounts for both the original CT image and its Gaussian scale space (GSS) filtered version to specify local and global signal properties, respectively. Each empirical marginal probability distribution of signals is closely approximated with a linear combination of discrete Gaussians (LCDG), containing two positive dominant and multiple sign-alternate subordinate DGs. The approximation is separated into two LCDGs to describe individually the lungs and their background, i.e., all other chest tissues. The second-order appearance submodel quantifies conditional pairwise intensity dependencies in the nearest voxel 26-neighborhood in both the original and GSS-filtered images. The shape submodel is built for a set of training data and is adapted during segmentation using both the lung and chest appearances. The accuracy of the proposed segmentation framework is quantitatively assessed using two public databases (ISBI VESSEL12 challenge and MICCAI LOLA11 challenge) and our own database with, respectively, 20, 55, and 30 CT images of various lung pathologies acquired with different scanners and protocols. Quantitative assessment of our framework in terms of Dice similarity coefficients, 95-percentile bidirectional Hausdorff distances, and percentage volume differences confirms the high accuracy of our model on both our database (98.4±1.0%, 2.2±1.0mm, 0.42±0.10%) and the VESSEL12 database (99.0±0.5%, 2.1±1.6mm, 0.39±0.20%), respectively. Similarly, the accuracy of our approach is further verified via a blind evaluation by the organizers of the LOLA11 competition, where an average overlap of 98.0% with the expert’s segmentation is yielded on all 55 subjects with our framework being ranked first among all the state-of-the-art techniques compared.

A framework for 3D kidney segmentation from abdominal computed tomography (CT) images is proposed. Accurate kidney segmentation from CT images is a challenging task due to the large inhomogeneity of the kidney (e.g., cortex and medulla), inter-patient anatomical differences, etc. To account for these challenges, a novel framework utilizing random forest (RF) classification that has the ability to cluster complex data is proposed. To build a robust classification model, discriminative features are needed for better separation of data classes. In this work, regional features from the CT appearance, a kidney shape prior model, and higher-order spatial interactions are extracted and are used for tissue classification. The shape model is constructed using a set of training images and is updated during segmentation using an appearance-based method taking into account both voxels' locations and appearances. The spatial interactions between CT data voxels are modeled using a higher-order spatial model that adds to the pairwise cliques the families of the triple- and quad cliques. The proposed framework has been tested on CT data that has been collected from 20 subjects and consist of multiple 3D CT scans acquired at the pre-and post-contrast agent administration. Evaluation results, using both volumetric and distance-based metrics, between manually drawn and automatically segmented contours confirm the high accuracy of the proposed technique.

In this paper, we propose a novel non-invasive framework for the early diagnosis of prostate cancer from diffusion-weighted magnetic resonance imaging (DW-MRI). The proposed approach consists of three main steps. In the first step, the prostate is localized and segmented based on a new level-set model. In the second step, the apparent diffusion coefficient (ADC) of the segmented prostate volume is mathematically calculated for different b-values. To preserve continuity, the calculated ADC values are normalized and refined using a Generalized Gauss-Markov Random Field (GGMRF) image model. The cumulative distribution function (CDF) of refined ADC for the prostate tissues at different b-values are then constructed. These CDFs are considered as global features describing water diffusion which can be used to distinguish between benign and malignant tumors. Finally, a deep learning auto-encoder network, trained by a stacked non-negativity constraint algorithm (SNCAE), is used to classify the prostate tumor as benign or malignant based on the CDFs extracted from the previous step. Preliminary experiments on 53 clinical DW-MRI data sets resulted in 100% correct classification, indicating the high accuracy of the proposed framework and holding promise of the proposed CAD system as a reliable non-invasive diagnostic tool.

Although renal biopsy remains the gold standard for diagnosing the type of renal rejection, it is not preferred due to its invasiveness, recovery time (1-2 weeks), and potential for complications, e.g., bleeding and/or infection. Therefore, there is an urgent need to explore a non-invasive technique that can early classify renal rejection types. In this paper, we develop a computer-aided diagnostic (CAD) system that can classify acute renal transplant rejection (ARTR) types early via the analysis of apparent diffusion coefficients (ADCs) extracted from diffusion-weighted (DW) MRI data acquired at low-(accounting for perfusion) and high-(accounting for diffusion) b-values. The developed framework mainly consists of three steps: (i) data co-alignment using a 3D B-spline-based approach (to handle local deviations due to breathing and heart beat motions) and segmentation of kidney tissue with an evolving geometric (level-set based) deformable model guided by a voxel-wise stochastic speed function, which follows a joint kidney-background Markov-Gibbs random field model accounting for an adaptive kidney shape prior and visual kidney-background appearances of DW-MRI data (image intensities and spatial interactions); (ii) construction of a cumulative empirical distribution of ADC at low and high b-values of the segmented kidney accounting for blood perfusion and water diffusion, respectively, to be our discriminatory ARTR types feature; and (iii) classification of ARTR types (acute tubular necrosis (ATN) anti-body- and T-cell-mediated rejection) based on deep learning of a non-negative constrained stacked autoencoder. Results show that 98% of the subjects were correctly classified in our “leave-one-subject-out” experiments on 39 subjects (namely, 8 out of 8 of the ATN group and 30 out of 31 of the T-cell group). Thus, the proposed approach holds promise as a reliable non-invasive diagnostic tool.

This paper proposes a novel framework for the identification of the radiation-induced lung injury (RILI) after radiation therapy (RT) using 4D computed tomography (CT) scans. The proposed methodology consists of four components: (i) elastic image registration; (ii) segmentation of the lung fields; (iii) extraction of functional and texture features; and (iv) classification of the lung tissues. The registration step locally aligns the consecutive phases of the respiratory cycle using an elastic image registration approach based on descent minimization of the sum of squared difference similarity metric. Secondly, lung fields are segmented using a hybrid framework that integrates an adaptive shape prior model, a first-order intensity model, and a second order homogeneity descriptor of the lung tissues. Next, regional features that describe both the texture features using the novel 7th-order Markov-Gibbs random field (MGRF) model in addition to the lung functionality features (e.g., ventilation and elasticity) are estimated from a segmented lungs. Finally, a random forest classifier (RF) is applied to distinguish between injured and normal lung tissues. To evaluate the proposed framework, we used data sets that have been collected from 13 patients who had underwent RT treatment. Experimental results demonstrate the promise of the proposed framework for the identification of the injured lung region, and thus hold the promise as a valuable tool for early detection of RILI.

This paper introduces a novel computer-aided diagnostic (CAD) system for the assessment of renal transplant status that integrates image-based biomarkers derived from 4D (3D + b -value) diffusion-weighted (DW) MRI, and clinical biomarkers. To analyze DW-MRI, our framework starts with kidney tissue segmentation using a level set approach after DW-MRI data alignment to handle the motion effects. Secondly, the cumulative empirical distributions (i.e., CDFs) of apparent diffusion coefficients (ADCs) of the segmented DW-MRIs are estimated at low and high gradient strengths and duration ( b -values) accounting for both blood perfusion and diffusion, respectively. Finally, these CDFs are fused with laboratory-based biomarkers (creatinine clearance and serum plasma creatinine) for the classification of transplant status using a deep learning-based classification approach utilizing a stacked non-negativity constrained auto-encoder. Using “leave-one-subject-out” experiments on a cohort of 58 subjects, the proposed CAD system distinguished non-rejection transplants from kidneys with abnormalities with a 95 % accuracy (sensitivity = 95 %, specificity = 94 %) and achieved a 95 % correct classification between early rejection and other kidney diseases. Our preliminary results demonstrate the promise of the proposed CAD system as a reliable non-invasive diagnostic tool for renal transplants assessment.

In this paper, we propose a novel framework for the automated extraction of the brain from T1-weighted MR images. The proposed approach is primarily based on the integration of a stochastic model [a two-level Markov-Gibbs random field (MGRF)] that serves to learn the visual appearance of the brain texture, and a geometric model (the brain isosurfaces) that preserves the brain geometry during the extraction process. The proposed framework consists of three main steps: 1) Following bias correction of the brain, a new three-dimensional (3-D) MGRF having a 26-pairwise interaction model is applied to enhance the homogeneity of MR images and preserve the 3-D edges between different brain tissues. 2) The nonbrain tissue found in the MR images is initially removed using the brain extraction tool (BET), and then the brain is parceled to nested isosurfaces using a fast marching level set method. 3) Finally, a classification step is applied in order to accurately remove the remaining parts of the skull without distorting the brain geometry. The classification of each voxel found on the isosurfaces is made based on the first- and second-order visual appearance features. The first-order visual appearance is estimated using a linear combination of discrete Gaussians (LCDG) to model the intensity distribution of the brain signals. The second-order visual appearance is constructed using an MGRF model with analytically estimated parameters. The fusion of the LCDG and MGRF, along with their analytical estimation, allows the approach to be fast and accurate for use in clinical applications. The proposed approach was tested on in vivo data using 300 infant 3-D MR brain scans, which were qualitatively validated by an MR expert. In addition, it was quantitatively validated using 30 datasets based on three metrics: the Dice coefficient, the 95% modified Hausdorff distance, and absolute brain volume difference. Results showed the capability of the proposed approach, outperforming four widely used BETs: BET, BET2, brain surface extractor, and infant brain extraction and analysis toolbox. Experiments conducted also proved that the proposed framework can be generalized to adult brain extraction as well.

This paper introduces a new framework for the segmentation of different brain structures from 3D infant MR brain images. The proposed segmentation framework is based on a shape prior built using a subset of co-aligned training images that is adapted during the segmentation process based on higher-order visual appearance characteristics of infant MRIs. These characteristics are described using voxel-wise image intensities and their spatial interaction features. In order to more accurately model the empirical grey level distribution of infant brain signals, a Linear Combination of Discrete Gaussians (LCDG) is used that has positive and negative components. Also to accurately account for the large inhomogeneity in infant MRIs, a higher-order Markov Gibbs Random Field (MGRF) spatial interaction model that integrates third- and fourth-order families with a traditional second-order model is proposed. The proposed approach was tested on 40 in-vivo infant 3D MR brain scans, having their ground truth created by an expert radiologist, using three metrics: the Dice coefficient, the 95-percentile modified Hausdorff distance, and the absolute brain volume difference. Experimental results promise an accurate segmentation of infant MR brain images compared to current open source segmentation tools.

Developing any non-invasive computer-aided diagnostic (CAD) system for the diagnosis of kidney diseases essentially requires the extraction of the kidney from medical images. We propose a shape based level-set framework for 3D kidney segmentation from diffusion-weighted magnetic resonance imaging (DW-MRI). A stochastic speed relationship is used to control the deformable model evolutions. This speed relationship is based on an adaptive shape prior guided by the first- and second-order visual appearance features of the DW-MRI data. These pre-mentioned image features are integrated into a joint Markov-Gibbs random field (MGRF) model of the kidney and its background. DW-MRI data sets from eight subjects acquired at different b-values ranging from 0 to 1000 s/mm2are tested using a leave-one-subject-out method to evaluate the proposed segmentation approach, and to compare its performance with other segmentation methods using three evaluation metrics: the Dice similarity coefficient (DSC), the 95-percentile modified Hausdorff distance, and the absolute kidney volume difference. Robustness and accuracy of the proposed approach are confirmed through the experimental results' evaluation between manually drawn and automatically segmented contours.

A novel framework for precise segmentation of pathological lung tissues from computed tomography (CT) is presented. The proposed segmentation method is based on a novel 3D joint Markov-Gibbs random field (MGRF) model that integrates three features: (i) the first-order visual appearance model of the CT image, (ii) the second-order spatial interaction model of the CT image, and (iii) a shape prior model of the lung. The first-order appearance model describes the empirical distribution of image signals using a linear combination of Discrete Gaussians (LCDG) with positive and negative components. The second order spatial interaction model describes the relation between the CT image signals using a pairwise MGRF spatial model of independent image signals and interdependent region labels. The shape prior is constructed from a set of training CT data, collected from different subjects. Experiments on 20 datasets with different types of pathologies confirm high accuracy of the proposed approach compared with other lung segmentation methods.

This paper presents a novel approach for extracting the brain from 3D T1-weighted MR images. The proposed approach combines a stochastic two-level Markov-Gibbs random field (MGRF) image model with a geometric model that parcels the brain into a set of nested iso-surfaces using a fast marching level setmethod. The classification of each brain voxel found on the iso-surfaces is performed based on the first-order (a linear combination of discrete gaussian (LCDG) model) and second-order (an MGRF model with analytically estimated parameters) visual appearance features of the brain structures. Our approach is tested on 280 infant 3D MR brain scans and evaluated on 9 data sets using the Dice coefficient, the 95-percentile modified Hausdorff distance, and absolute brain volume difference. Experimental results showed that the fusion of the stochastic and geometric models of brain MRI data has led to more accurate brain extraction, when compared with other widely-used brain extraction tools, such as BET, BET2, and brain surface extractor (BSE).

This paper introduces a new adaptive atlas-based framework for the automated segmentation of different brain structures from infant diffusion tensor images (DTI). To model the brain images and their desired region maps, we used a joint Markov-Gibbs random field (MGRF) model that accounts for three image descriptors: (i) a 1st-order visual appearance to describe the empirical distribution of DTI extracted features, (ii) an adaptive shape model, and (iii) a 3D spatially invariant 2nd-order MGRF homogeneity descriptor. The 1st-order visual appearance descriptor is accurately modeled using a linear combination of discrete Gaussians (LCDG) model having positive and negative components. The proposed adaptive shape model is constructed from a prior atlas database built using a subset of co-aligned training data sets that is adapted during the segmentation process guided by the visual appearance characteristics of several DTI features. To accurately account for the large inhomogeneity of infant brains, the homogeneity descriptor is modeled by a 2nd-order translation and rotation invariant MGRF of region labels with analytically estimated potentials. The high accuracy of our segmentation approach was confirmed by testing it on 10 in-vivo infant DTI brain data sets using three metrics: the Dice similarity coefficient, the 95-percentile modified Hausdorff distance, and the absolute brain volume difference.

A novel framework for assessing wall thickening from 4D cine cardiac magnetic resonance imaging (CMRI) is proposed. The proposed approach is primarily based on using geometrical features to track the left ventricle (LV) wall during the cardiac cycle. The 4D tracking approach consists of the following two main steps: (i) Initially, the surface points on the LV wall are tracked by solving a 3D Laplace equation between two successive LV surfaces; and (ii) Secondly, the locations of the tracked LV surface points are iteratively adjusted through an energy minimization cost function using a generalized Gauss-Markov random field (GGMRF) image model in order to remove inconsistencies and preserve the anatomy of the heart wall during the tracking process. Then the myocardial wall thickening is estimated by co-allocation of the corresponding points, or matches between the endocardium and epicardium surfaces of the LV wall using the solution of the 3D Laplace equation. Experimental results on in vivo data confirm the accuracy and robustness of our method. Moreover, the comparison results demonstrate that our approach outperforms 2D wall thickening estimation approaches.

A novel framework for the classification of acute rejection versus nonrejection status of renal transplants from 2-D dynamic contrast-enhanced magnetic resonance imaging is proposed. The framework consists of four steps. First, kidney objects are segmented from adjacent structures with a level set deformable boundary guided by a stochastic speed function that accounts for a fourth-order Markov-Gibbs random field model of the kidney/background shape and appearance. Second, a Laplace-based nonrigid registration approach is used to account for local deformations caused by physiological effects. Namely, the target kidney object is deformed over closed, equispaced contours (iso-contours) to closely match the reference object. Next, the cortex is segmented as it is the functional kidney unit that is most affected by rejection. To characterize rejection, perfusion is estimated from contrast agent kinetics using empirical indexes, namely, the transient phase indexes (peak signal intensity, time-to-peak, and initial up-slope), and a steady-phase index defined as the average signal change during the slowly varying tissue phase of agent transit. We used a kn-nearest neighbor classifier to distinguish between acute rejection and nonrejection. Performance of our method was evaluated using the receiver operating characteristics (ROC). Experimental results in 50 subjects, using a combinatoric kn-classifier, correctly classified 92% of training subjects, 100% of the test subjects, and yielded an area under the ROC curve that approached the ideal value. Our proposed framework thus holds promise as a reliable noninvasive diagnostic tool.

A novel non-invasive approach for the early diagnosis of prostate cancer from diffusion-weighted MRI is proposed. The proposed diagnostic approach consists of three main steps. The first step is to isolate the prostate from the surrounding anatomical structures based on a Maximum a Posteriori (MAP) estimate of a new log-likelihood function that accounts for the shape priori, the spatial interaction, and the current appearance of prostate tissues and its background (surrounding anatomical structures). In the second step, a nonrigid registration algorithm is employed to account for any local deformation between the segmented prostates at different b-values that could occur during the scanning process due to patient breathing and local motion. In the final step, a kn-Nearest Neighbor-based classifier is used to classify the prostate into benign or malignant based on four appearance features extracted from registered images. Moreover, in this paper we introduce a new approach to generate color maps that illustrate the propagation of diffusion in prostate tissues based on the analysis of the 3D spatial interaction of the change of the gray level values of prostate voxel using a Generalized Gauss-Markov Random Field (GGMRF) image model. Finally, the tumor boundaries are determined using a level set deformable model controlled by the diffusion information and the spatial interactions between the prostate voxels. Experimental results on 28 clinical diffusion-weighted MRI data sets yield promising results.

Accurate registration of cardiac first-pass magnetic resonance imaging (FP-MRI) is fundamental for precise analysis of myocardial perfusion. In this paper, we introduce and validate a new framework for accurate registration of the segmented left ventricle (LV) wall on cardiac FP-MRI. Due to the continuous physiological motion of the heart that causes the LV wall to change shape significantly and to move within and through the image plane, we developed a new methodology for 2D FP-MRI nonrigid registration that includes: (i) global target-to-reference frame-to-frame alignment based on the maximization of the normalized mutual information (NMI); (ii) local alignment based on using a B-splines transformation model that maximizes a similarity function that accounts for 1st- and 2nd-order NMI between the globally aligned frames followed by (iii) a refinement step that is based on deforming each pixel of the target wall over evolving closed equi-spaced contours (iso-contours) to closely match the reference wall. Respective iso-contours in both reference and target frames are matched based on solving the Laplace equation. We have tested our framework on both synthetic phantoms and 20 in-vivo data sets that have been collected from patients with ischemic damage from heart attacks, who are undergoing a novel myoregeneration therapy.

To reduce noise within a tag line, unsharpen the tag edges in spatial domain, and amplify the tag-to-background contrast, a 3D energy minimization framework for the enhancement of tagged Cardiac Magnetic Resonance (CMR) image sequences, based on learning first- and second-order visual appearance models, is proposed. The first-order appearance modeling uses adaptive Linear Combinations of Discrete Gaussians (LCDG) to accurately approximate the empirical marginal probability distribution of CMR signals for a given sequence, and separates tag and background submodels. It is also used to classify the tag lines and the background. The second-order model considers image sequences as samples of a translation- and rotation-invariant 3D Markov-Gibbs Random Field (MGRF) with multiple pairwise voxel interactions. A 3D energy function for this model is built by using the analytical estimation of the spatio-temporal geometry and Gibbs potentials of interaction. To improve the strain estimation, by enhancing the tag and background homogeneity and contrast, the given sequence is adjusted using comparisons to the energy minimizer. Special 3D geometric phantoms, motivated by statistical analysis of the tagged CMR data, have been designed to validate the accuracy of our approach. Experiments with the phantoms and eight real data sets have confirmed the high accuracy of the functional parameters that are estimated for the enhanced tagged sequences when using popular spectral techniques, such as spectral Harmonic Phase (HARP).

Prostate segmentation is an essential step in developing any non-invasive Computer-Assisted Diagnostic (CAD) system for the early diagnosis of prostate cancer using Magnetic Resonance Images (MRI). In this paper, a novel framework for 3D segmentation of the prostate region from Diffusion-Weighted Magnetic Resonance Imaging (DW-MRI) is proposed. The framework is based on a Maximum A Posteriori (MAP) estimate of a new log-likelihood function that accounts for Markov-Gibbs shape and appearance models of the object-of-interest and its background. The framework was evaluated on in vivo prostate DW-MRI with available manual expert segmentation. The performance evaluation of the proposed segmentation approach, based on voxel-based and distance-based metrics between manually drawn and automatically segmented contours, confirmed the robustness and accuracy of the proposed segmentation approach.

A new automatic approach for the estimation of global indexes from short-axis cine cardiac magnetic resonance (CMR) images is proposed. The inner contour of the left ventricle (LV) is segmented with a level set-based deformable model. Its evolution is controlled by a specially designed stochastic speed function that accounts for a learned spatially variant statistical shape prior, a 1st-order visual appearance descriptor of the contour interior and exterior (associated with the object and background, respectively), and a spatially invariant 2nd-order homogeneity descriptor. After the inner contour delineation, the total cavity volume (time varying LV volume) data is used to estimate the LV global functional indexes, i.e., ejection fraction, systolic and diastolic slopes. Experiments with in-vivo CMR data, obtained from subjects with chronic ischemic heart disease and damage that is documented by viability MRI, confirm a high robustness and accuracy of the proposed approach.

Kidney segmentation is an essential step in developing any non-invasive Computer-Assisted Diagnostic (CAD) system for the early detection of acute renal rejection. This paper describes a 3-D approach for kidney segmentation from abdominal Computed Tomography (CT) images using a level set-based deformable model. Its evolution is controlled by a specially designed stochastic speed function that accounts for a shape prior and features of image intensity and spatial interactions. The shape prior is learned from the co-aligned 3-D kidney data. The current visual appearances are described with marginal gray level distributions obtained by separating their mixture over the kidney data. The spatial interactions between the kidney voxels are modeled by a 3-D 2nd-order translation and rotation variant Markov-Gibbs Random Field (MGRF) of “object-background” labels with analytically estimated potentials. The proposed approach has been evaluated on the CT data sets of 29 patients, yielding an average volumetric overlap error of 3.71%. The presented results indicate that combing CT images' characteristics into level set evolution leads to more accurate segmentation results.

To discriminate more accurately between dyslexic and normal brains, we detect the brain cortex variability through a spherical harmonic analysis that represents a 3D surface supported by the unit sphere, having a linear combination of special basis functions, called spherical harmonics (SHs). The proposed 3D shape analysis is carried out in five steps: (i) 3D brain cortex segmentation, with a deformable 3D boundary, controlled by two probabilistic visual appearance models (the learned prior and the estimated current appearance one); (ii) 3D Delaunay triangulation to construct a 3D mesh model of the brain cortex surface; (iii) mapping this model to the unit sphere; (iv) computing the SHs for the surface, and (v) determining the number of the SHs to delineate the brain cortex. We describe the brain shape complexity with a new shape index, the estimated number of the SHs, and use it for the K-nearest classification into the normal and dyslexic brains. Initial experiments suggest that our shape index is a promising supplement to the current dyslexia diagnostic techniques.

Our long-term research goal is to develop a fully automated, image-based diagnostic system for early diagnosis of pulmonary nodules that may lead to lung cancer. This paper focuses on validating our approach for monitoring the development of lung nodules detected in successive chest low dose computed tomography (LDCT) scans of a patient. Our methodology for monitoring the detected lung nodules includes 3-D LDCT data registration, which is non-rigid and involves two steps: (i) global target-to-prototype alignment of one scan to another using the learned prior appearance model followed by (ii) local alignment in order to correct for intricate relative deformations. This approach has been validated on elastic lung phantoms constructed using state-of-the-art microfluidics technology. The elastic lung phantoms are fabricated from a flexible transparent polymer, i.e., polydimethylsiloxane (PDMS). These Phantoms mimic the contractions and expansions of the lung and nodules seen during normal breathing. Experiments confirm the high accuracy of the proposed approach for measuring the growth rate of the detected lung nodules.

A new speed function to guide evolution of a level-set based active contour is proposed for segmenting an object from its background in a given image. The guidance accounts for a learned spatially variant statistical shape prior, 1st-order visual appearance descriptors of the contour interior and exterior (associated with the object and background, respectively), and a spatially invariant 2nd-order homogeneity descriptor. The shape prior is learned from a subset of co-aligned training images. The visual appearances are described with marginal gray level distributions obtained by separating their mixture over the image. The evolving contour interior is modeled by a 2nd-order translation and rotation invariant Markov-Gibbs random field of object / background labels with analytically estimated potentials. Experiments to segment the inner cavity of heart cine images confirm robustness and accuracy of the proposed approach.

A new speed function to guide evolution of a level-set based active contour is proposed for segmenting an object from its background in a given image. The guidance accounts for a learned spatially variant statistical shape prior, 1st-order visual appearance descriptors of the contour interior and exterior (associated with the object and background, respectively), and a spatially invariant 2nd-order homogeneity descriptor. The shape prior is learned from a subset of co-aligned training images. The visual appearances are described with marginal gray level distributions obtained by separating their mixture over the image. The evolving contour interior is modeled by a 2nd-order translation and rotation invariant Markov-Gibbs random field of object/background labels with analytically estimated potentials. Experiments with kidney CT images confirm robustness and accuracy of the proposed approach.